Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008310.1 Hibiscus syriacus cultivar Beakdansim tig00111000_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3887810
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 15
Found at i:1918911 original size:35 final size:37
Alignment explanation
Indices: 1918842--1918915 Score: 116
Period size: 35 Copynumber: 2.1 Consensus size: 37
1918832 ATACTATTTC
*
1918842 CATCACCATAATCCATCTTCCATTATCACACCTATAT
1 CATCACCATAATCCATCTACCATTATCACACCTATAT
*
1918879 CATCACCATAGTCCATC-ACCA-TATCACACCTATAT
1 CATCACCATAATCCATCTACCATTATCACACCTATAT
1918914 CA
1 CA
1918916 CCATCACTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 16 0.46
36 3 0.09
37 16 0.46
ACGTcount: A:0.34, C:0.36, G:0.01, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACACCTATAT
Found at i:1918915 original size:11 final size:10
Alignment explanation
Indices: 1918865--1918916 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 10
1918855 CATCTTCCAT
1918865 TATCACACCTA
1 TATCACACC-A
1918876 TATCATCACCA
1 TATCA-CACCA
1918887 TAGTCCATCACCA
1 TA-T-CA-CACCA
1918900 TATCACACCTA
1 TATCACACC-A
1918911 TATCAC
1 TATCAC
1918917 CATCACTCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
10 4 0.11
11 17 0.46
12 6 0.16
13 10 0.27
ACGTcount: A:0.35, C:0.37, G:0.02, T:0.27
Consensus pattern (10 bp):
TATCACACCA
Found at i:1923951 original size:27 final size:27
Alignment explanation
Indices: 1923921--1923984 Score: 128
Period size: 27 Copynumber: 2.4 Consensus size: 27
1923911 TTTCAACACA
1923921 CTCATCTTCATTCTCAATGCTCTTACT
1 CTCATCTTCATTCTCAATGCTCTTACT
1923948 CTCATCTTCATTCTCAATGCTCTTACT
1 CTCATCTTCATTCTCAATGCTCTTACT
1923975 CTCATCTTCA
1 CTCATCTTCA
1923985 ATTACTCGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.19, C:0.34, G:0.03, T:0.44
Consensus pattern (27 bp):
CTCATCTTCATTCTCAATGCTCTTACT
Found at i:1928158 original size:22 final size:20
Alignment explanation
Indices: 1928118--1928164 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 20
1928108 TGTAGGAGTC
1928118 TTTTTCTTTTCTTTATGTTT
1 TTTTTCTTTTCTTTATGTTT
1928138 TTTTTCTTCTTTCTTGT-TGTTT
1 TTTTTC-T-TTTCTT-TATGTTT
1928160 TTTTT
1 TTTTT
1928165 GTTGTAGCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.25
21 1 0.04
22 16 0.67
23 1 0.04
ACGTcount: A:0.02, C:0.11, G:0.06, T:0.81
Consensus pattern (20 bp):
TTTTTCTTTTCTTTATGTTT
Found at i:1928582 original size:36 final size:36
Alignment explanation
Indices: 1928541--1928689 Score: 199
Period size: 36 Copynumber: 4.1 Consensus size: 36
1928531 ATTTATAAGT
* * * *
1928541 TGGTGATAATATGGGCGTGATAATGGTGGTGGAATA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
* *
1928577 TGGTGACGATATAGGCGTGATAATGGAGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
* * *
1928613 TGGTGATGATAAAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
* *
1928649 TGGTGATGATATAGGCATGATAATGGAGATGGAAGA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
1928685 TGGTG
1 TGGTG
1928690 TTGGACAGAT
Statistics
Matches: 99, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 99 1.00
ACGTcount: A:0.30, C:0.05, G:0.38, T:0.28
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
Found at i:1931251 original size:14 final size:13
Alignment explanation
Indices: 1931234--1931283 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
1931224 GTGCAAAAAG
1931234 AAAGAAAAAGACAA
1 AAAGAAAAAGA-AA
*
1931248 AAAGAAGAAGAAA
1 AAAGAAAAAGAAA
1931261 AGAAG-AAAAG--A
1 A-AAGAAAAAGAAA
1931272 AAAGAAAAAGAA
1 AAAGAAAAAGAA
1931284 TTCAAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
10 3 0.10
11 7 0.23
13 7 0.23
14 13 0.43
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:1931280 original size:19 final size:18
Alignment explanation
Indices: 1931228--1931283 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 18
1931218 ATTGGAGTGC
1931228 AAAAAG-AAAGAAAAAGA
1 AAAAAGAAAAGAAAAAGA
1931245 CAAAAAGAAGAAG-AAAAGA
1 -AAAAAGAA-AAGAAAAAGA
1931264 AGAAAAGAAAAGAAAAAGA
1 A-AAAAGAAAAGAAAAAGA
1931283 A
1 A
1931284 TTCAAAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 10 0.29
19 21 0.62
20 3 0.09
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAAGA
Found at i:1935231 original size:33 final size:33
Alignment explanation
Indices: 1935152--1935255 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
1935142 ATACAATCTG
* *
1935152 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
1935188 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
1935221 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
1935254 TC
1 TC
1935256 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:1939046 original size:24 final size:21
Alignment explanation
Indices: 1939012--1939054 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
1939002 TGCACAAGAT
*
1939012 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
1939034 ATGTACCTATTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
1939055 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:1958862 original size:11 final size:12
Alignment explanation
Indices: 1958797--1958864 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
1958787 ATTTTGGTTT
1958797 TTTTTTTTTG-C
1 TTTTTTTTTGCC
1958808 TTTTTTTTGTGCC
1 TTTTTTTT-TGCC
* *
1958821 -TTTTCTTTACC
1 TTTTTTTTTGCC
1958832 -TTTTTTTTGCC
1 TTTTTTTTTGCC
**
1958843 TTTTTTTTTGTT
1 TTTTTTTTTGCC
1958855 TTTTTTTTTG
1 TTTTTTTTTG
1958865 AAAAAAAAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
11 20 0.42
12 27 0.56
13 1 0.02
ACGTcount: A:0.01, C:0.12, G:0.09, T:0.78
Consensus pattern (12 bp):
TTTTTTTTTGCC
Found at i:1960289 original size:24 final size:23
Alignment explanation
Indices: 1960261--1960320 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 23
1960251 ACTTTTTTTT
1960261 CTTTCTTTTTCTTCTTTTCGAGTG
1 CTTTCTTTTTCTTCTTTT-GAGTG
*
1960285 CTTTCAATTTT-TTCTTTTGAGTG
1 CTTTC-TTTTTCTTCTTTTGAGTG
1960308 CTTT-TATTTTCTT
1 CTTTCT-TTTTCTT
1960321 TGCTGATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
22 4 0.13
23 11 0.35
24 12 0.39
25 4 0.13
ACGTcount: A:0.08, C:0.17, G:0.10, T:0.65
Consensus pattern (23 bp):
CTTTCTTTTTCTTCTTTTGAGTG
Found at i:1962194 original size:8 final size:8
Alignment explanation
Indices: 1962181--1962242 Score: 54
Period size: 8 Copynumber: 7.0 Consensus size: 8
1962171 ATTTTTTTTT
1962181 CAAAAAAA
1 CAAAAAAA
1962189 C-AAAAAA
1 CAAAAAAA
1962196 CAAAAAAA
1 CAAAAAAA
1962204 GGCAAAAAAAAAA
1 --C---AAAAAAA
1962217 CAAAAAAA
1 CAAAAAAA
1962225 GGCAAAAAAA
1 --CAAAAAAA
1962235 CAAAAAAA
1 CAAAAAAA
1962243 GAGCCAAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 16
0.74 0.00 0.26
Matches are distributed among these distances:
7 7 0.15
8 22 0.48
10 9 0.20
11 1 0.02
13 7 0.15
ACGTcount: A:0.82, C:0.11, G:0.06, T:0.00
Consensus pattern (8 bp):
CAAAAAAA
Found at i:1962216 original size:21 final size:21
Alignment explanation
Indices: 1962185--1962253 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
1962175 TTTTTTCAAA
1962185 AAAACAAAAAACAAAAAAAGGC
1 AAAA-AAAAAACAAAAAAAGGC
1962207 AAAAAAAAAACAAAAAAAGGC
1 AAAAAAAAAACAAAAAAAGGC
* * *
1962228 AAAAAAACAA-AAAAAGAGCC
1 AAAAAAAAAACAAAAAAAGGC
1962248 AAAAAA
1 AAAAAA
1962254 GCCAAAATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
20 14 0.32
21 26 0.59
22 4 0.09
ACGTcount: A:0.80, C:0.12, G:0.09, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAACAAAAAAAGGC
Found at i:1969105 original size:11 final size:13
Alignment explanation
Indices: 1969075--1969104 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1969065 TGGCCAAAGA
1969075 TGAAAAGGTGTGT
1 TGAAAAGGTGTGT
1969088 TGAAAAGGTGTG-
1 TGAAAAGGTGTGT
1969100 TGAAA
1 TGAAA
1969105 GATGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.37, C:0.00, G:0.37, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTGTGT
Found at i:1972495 original size:19 final size:20
Alignment explanation
Indices: 1972454--1972504 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
1972444 GAAACCCCTT
*
1972454 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
1972474 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
1972493 TGAAGATACATG
1 TGAAAATACATG
1972505 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:1973442 original size:30 final size:31
Alignment explanation
Indices: 1973403--1973462 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
1973393 ACATGCTGCC
**
1973403 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
* *
1973434 ATGA-ATCTAAAACATATGTAAGCATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
1973463 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:1992672 original size:17 final size:17
Alignment explanation
Indices: 1992650--1992682 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1992640 GTCGGCTAAA
*
1992650 AGAAATGGTTATGGTAT
1 AGAAATGGATATGGTAT
1992667 AGAAATGGATATGGTA
1 AGAAATGGATATGGTA
1992683 AAGGTAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.30, T:0.30
Consensus pattern (17 bp):
AGAAATGGATATGGTAT
Found at i:1995089 original size:15 final size:16
Alignment explanation
Indices: 1995062--1995098 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
1995052 CTTTATTATC
1995062 TTATTTCATCTTTCGT
1 TTATTTCATCTTTCGT
*
1995078 TTATTT-ATCTTTTGT
1 TTATTTCATCTTTCGT
1995093 TTATTT
1 TTATTT
1995099 TATTCTAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.14, C:0.11, G:0.05, T:0.70
Consensus pattern (16 bp):
TTATTTCATCTTTCGT
Found at i:1995475 original size:17 final size:18
Alignment explanation
Indices: 1995453--1995500 Score: 73
Period size: 17 Copynumber: 2.7 Consensus size: 18
1995443 TTTTTTTTCA
1995453 AAAAAACAAAAAAAAGG-
1 AAAAAACAAAAAAAAGGC
1995470 AAAAAA-AAACAAAAAGGC
1 AAAAAACAAA-AAAAAGGC
1995488 AAAAAACAAAAAA
1 AAAAAACAAAAAA
1995501 GCCAAAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
16 3 0.11
17 13 0.46
18 9 0.32
19 3 0.11
ACGTcount: A:0.83, C:0.08, G:0.08, T:0.00
Consensus pattern (18 bp):
AAAAAACAAAAAAAAGGC
Found at i:1995507 original size:15 final size:15
Alignment explanation
Indices: 1995473--1995507 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1995463 AAAAAGGAAA
*
1995473 AAAAAACAAAAAGGC
1 AAAAAACAAAAAAGC
1995488 AAAAAACAAAAAAGCC
1 AAAAAACAAAAAAG-C
1995504 AAAA
1 AAAA
1995508 TTTCAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.77, C:0.14, G:0.09, T:0.00
Consensus pattern (15 bp):
AAAAAACAAAAAAGC
Found at i:1999798 original size:15 final size:16
Alignment explanation
Indices: 1999771--1999807 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
1999761 CTTTATTATC
1999771 TTATTTCATCTTTCGT
1 TTATTTCATCTTTCGT
*
1999787 TTATTT-ATCTTTTGT
1 TTATTTCATCTTTCGT
1999802 TTATTT
1 TTATTT
1999808 TATTCAATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.14, C:0.11, G:0.05, T:0.70
Consensus pattern (16 bp):
TTATTTCATCTTTCGT
Found at i:2007555 original size:17 final size:18
Alignment explanation
Indices: 2007535--2007576 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
2007525 AAATTTTAGC
*
2007535 GTTTTTTTG-GTTTTTTT
1 GTTTTTTTGCATTTTTTT
2007552 GTTTTTTTGCATTTTTTT
1 GTTTTTTTGCATTTTTTT
2007570 -TTTTTTT
1 GTTTTTTT
2007577 TTTTAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.70
18 7 0.30
ACGTcount: A:0.02, C:0.02, G:0.12, T:0.83
Consensus pattern (18 bp):
GTTTTTTTGCATTTTTTT
Found at i:2007559 original size:8 final size:8
Alignment explanation
Indices: 2007535--2007580 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 8
2007525 AAATTTTAGC
2007535 GTTTTTTT
1 GTTTTTTT
2007543 GGTTTTTTT
1 -GTTTTTTT
2007552 GTTTTTTT
1 GTTTTTTT
2007560 GCATTTTTTT
1 G--TTTTTTT
2007570 -TTTTTTT
1 GTTTTTTT
2007577 -TTTT
1 GTTTT
2007581 AAAATAGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
7 11 0.31
8 9 0.26
9 8 0.23
10 7 0.20
ACGTcount: A:0.02, C:0.02, G:0.11, T:0.85
Consensus pattern (8 bp):
GTTTTTTT
Found at i:2007946 original size:15 final size:16
Alignment explanation
Indices: 2007926--2007962 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
2007916 GATTAGAATA
2007926 AAATAAACAAAAGAT-
1 AAATAAACAAAAGATG
*
2007941 AAATAAACAGAAGATG
1 AAATAAACAAAAGATG
2007957 AAATAA
1 AAATAA
2007963 GATAATAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.70, C:0.05, G:0.11, T:0.14
Consensus pattern (16 bp):
AAATAAACAAAAGATG
Found at i:2017199 original size:901 final size:900
Alignment explanation
Indices: 2015460--2017250 Score: 3528
Period size: 901 Copynumber: 2.0 Consensus size: 900
2015450 AAACATGATC
2015460 AAATAAGCATAGGATGAAAATAATAATATGATAATTTATACTAACATGTGAATGCATGCTTATGA
1 AAATAAGCATAGGATGAAAATAATAATATGATAATTTATACTAACATGTGAATGCATGCTTATGA
2015525 TAGAATATAATGTATAAATGATATAGTATAAGATAGGGTAATGAAGAATTCCCTTAGAAACATCT
66 TAGAATATAATGTATAAATGATATAGTATAAGATAGGGTAATGAAGAATTCCCTTAGAAACATCT
2015590 ATGAAGAACATCCATGGTGTGTTCAAGTCATGGAGAAAGTTGGAGCTTGTTTGGATCGTATCATC
131 ATGAAGAACATCCATGGTGTGTTCAAGTCATGGAGAAAGTTGGAGCTTGTTTGGATCGTATCATC
2015655 CTCCCCTTCTTTTAGGCGATTTGTCCTCAAATCGAAGTAGTTTCTCATTGAATACCTTCTTGATG
196 CTCCCCTTCTTTTAGGCGATTTGTCCTCAAATCGAAGTAGTTTCTCATTGAATACCTTCTTGATG
*
2015720 TAGGAAGGATTGAATCCTCAACCTCTTGGCTTCAAATCTGGTAACTTCTCGTCCTTTGATGGGAG
261 TAGGAAGGATTGAATCCTCAACCTCTTGGCTTCAAATCTGGTAACTTCTCATCCTTTGATGGGAG
2015785 GACACAATGTTTAAGAACCATCACATGTCCTTTGAATGGAAAAGACATATCCCTTCACGAACCAA
326 GACACAATGTTTAAGAACCATCACATGTCCTTTGAATGGAAAAGACATATCCCTTCACGAACCAA
*
2015850 CTTGATCCTTTTACTTTATTCTTTGAATAATCACAATGCTTGGAAATGACCTCTATCTCTTCAAT
391 CTTGATCCTTTTACTTTATTCTTTGAATAATCACAATGCTTGGAAAGGACCTCTATCTCTTCAAT
*
2015915 TCCTCCTTTTAATTCACCATGCTTGTTGGTGAAAAGGTTTGTCTCCTGGTTGGAGTCATCACATC
456 TCCTCCTTTTAATTCACCATGCTTGTTGGTGAAAAAGTTTGTCTCCTGGTTGGAGTCATCACATC
2015980 TCTTGGTGAAAATAATTGTTCTTTGAATGACTCCTTGGTGCTGATTTAAATCATCATGCCCTTTC
521 TCTTGGTGAAAATAATTGTTCTTTGAATGACTCCTTGGTGCTGATTTAAATCATCATGCCCTTTC
2016045 ACCATTGTGTCTCTCCAAATTATTGCCTTGAAGGTTGGTATGATTTCTTCACCATAAGGATGAAA
586 ACCATTGTGTCTCTCCAAATTATTGCCTTGAAGGTTGGTATGATTTCTTCACCATAAGGATGAAA
2016110 CAAGTTGCTGCAAAATAAATCAAAGTTAGTAAATGAAAAACTATTAACAAGGTGAATGGAAATAG
651 CAAGTTGCTGCAAAATAAATCAAAGTTAGTAAATGAAAAACTATTAACAAGGTGAATGGAAATAG
*
2016175 CAAACCAGGGTAGATGTTTAATGGGCATTGGTTGCTTGATGGAAAACTCTATTGGTTGTTGAAAT
716 CAAACCAGGGTAGATGTTTAATGGGCATTGGATGCTTGATGGAAAACTCTATTGGTTGTTGAAAT
2016240 CTCTTCAATAGTTATAATGTACTTGGAGCCTCAATGATCACAACTTGTGGCACTTCAAGTGACAC
781 CTCTTCAATAGTTATAATGTACTTGGAGCCTCAATGATCACAACTTGTGGCACTTCAAGTGACAC
2016305 ATCTTTTTGAACTTCTAGAGACATAATTGTTGGAACCTCAAAGGATATAGTATGA
846 ATCTTTTTGAACTTCTAGAGACATAATTGTTGGAACCTCAAAGGATATAGTATGA
2016360 AAATAAGCATAGGATGAAAATAATAATATGATAATTTATACTAACATGTGAATGCATGCTTATGA
1 AAATAAGCATAGGATGAAAATAATAATATGATAATTTATACTAACATGTGAATGCATGCTTATGA
2016425 TAGAATATAATGTATAAATGATATAGTATAAGATAGGGTAATGAAGAATTCCCTTAGAAACATCT
66 TAGAATATAATGTATAAATGATATAGTATAAGATAGGGTAATGAAGAATTCCCTTAGAAACATCT
2016490 ATGAAGAACATCCATGGTGTGTTCAAGTCATGGAGAAAGTTGGAGCTTGTTTGGATCGTATCATC
131 ATGAAGAACATCCATGGTGTGTTCAAGTCATGGAGAAAGTTGGAGCTTGTTTGGATCGTATCATC
2016555 CTCCCCTTCTTTTAGGCGATTTGTCCTCAAAATCGAAGTAGTTTCTCATTGAATACCTTCTTGAT
196 CTCCCCTTCTTTTAGGCGATTTGTCCTC-AAATCGAAGTAGTTTCTCATTGAATACCTTCTTGAT
2016620 GTAGGAAGGATTGAATCCTCAACCTCTTGGCTTCAAATCTGGTAACTTCTCATCCTTTGATGGGA
260 GTAGGAAGGATTGAATCCTCAACCTCTTGGCTTCAAATCTGGTAACTTCTCATCCTTTGATGGGA
2016685 GGACACAATGTTTAAGAACCATCACATGTCCTTTGAATGGAAAAGACATATCCCTTCACGAACCA
325 GGACACAATGTTTAAGAACCATCACATGTCCTTTGAATGGAAAAGACATATCCCTTCACGAACCA
2016750 ACTTGATCCTTTTACTTTATTCTTTGAATAATCACAATGCTTGGAAAGGACCTCTATCTCTTCAA
390 ACTTGATCCTTTTACTTTATTCTTTGAATAATCACAATGCTTGGAAAGGACCTCTATCTCTTCAA
2016815 TTCCTCCTTTTAATTCACCATGCTTGTTGGTGAAAAAGTTTGTCTCCTGGTTGGAGTCATCACAT
455 TTCCTCCTTTTAATTCACCATGCTTGTTGGTGAAAAAGTTTGTCTCCTGGTTGGAGTCATCACAT
2016880 CTCTTGGTGAAAATAATTGTTCTTTGAATGACTCCTTGGTGCTGATTTAAATCATCATGCCCTTT
520 CTCTTGGTGAAAATAATTGTTCTTTGAATGACTCCTTGGTGCTGATTTAAATCATCATGCCCTTT
2016945 CACCATTGTGTCTCTCCAAATTATTGCCTTGAAGGTTGGTATGATTTCTTCACCATAAGGATGAA
585 CACCATTGTGTCTCTCCAAATTATTGCCTTGAAGGTTGGTATGATTTCTTCACCATAAGGATGAA
2017010 ACAAGTTGCTGCAAAATAAATCAAAGTTAGTAAATGAAAAACTATTAACAAGGTGAATGGAAATA
650 ACAAGTTGCTGCAAAATAAATCAAAGTTAGTAAATGAAAAACTATTAACAAGGTGAATGGAAATA
2017075 GCAAACCAGGGTAGATGTTTAATGGGCATTGGATGCTTGATGGAAAACTCTATTGGTTGTTGAAA
715 GCAAACCAGGGTAGATGTTTAATGGGCATTGGATGCTTGATGGAAAACTCTATTGGTTGTTGAAA
*
2017140 TCTCTTCAATAGTTATAATGTACTTGGAGCCTGAATGATCACAACTTGTGGCACTTCAAGTGACA
780 TCTCTTCAATAGTTATAATGTACTTGGAGCCTCAATGATCACAACTTGTGGCACTTCAAGTGACA
2017205 CATCTTTTTGAACTTCTAGAGACATAATTGTTGGAACCTCAAAGGA
845 CATCTTTTTGAACTTCTAGAGACATAATTGTTGGAACCTCAAAGGA
2017251 CATGTCTTAT
Statistics
Matches: 885, Mismatches: 5, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
900 223 0.25
901 662 0.75
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Consensus pattern (900 bp):
AAATAAGCATAGGATGAAAATAATAATATGATAATTTATACTAACATGTGAATGCATGCTTATGA
TAGAATATAATGTATAAATGATATAGTATAAGATAGGGTAATGAAGAATTCCCTTAGAAACATCT
ATGAAGAACATCCATGGTGTGTTCAAGTCATGGAGAAAGTTGGAGCTTGTTTGGATCGTATCATC
CTCCCCTTCTTTTAGGCGATTTGTCCTCAAATCGAAGTAGTTTCTCATTGAATACCTTCTTGATG
TAGGAAGGATTGAATCCTCAACCTCTTGGCTTCAAATCTGGTAACTTCTCATCCTTTGATGGGAG
GACACAATGTTTAAGAACCATCACATGTCCTTTGAATGGAAAAGACATATCCCTTCACGAACCAA
CTTGATCCTTTTACTTTATTCTTTGAATAATCACAATGCTTGGAAAGGACCTCTATCTCTTCAAT
TCCTCCTTTTAATTCACCATGCTTGTTGGTGAAAAAGTTTGTCTCCTGGTTGGAGTCATCACATC
TCTTGGTGAAAATAATTGTTCTTTGAATGACTCCTTGGTGCTGATTTAAATCATCATGCCCTTTC
ACCATTGTGTCTCTCCAAATTATTGCCTTGAAGGTTGGTATGATTTCTTCACCATAAGGATGAAA
CAAGTTGCTGCAAAATAAATCAAAGTTAGTAAATGAAAAACTATTAACAAGGTGAATGGAAATAG
CAAACCAGGGTAGATGTTTAATGGGCATTGGATGCTTGATGGAAAACTCTATTGGTTGTTGAAAT
CTCTTCAATAGTTATAATGTACTTGGAGCCTCAATGATCACAACTTGTGGCACTTCAAGTGACAC
ATCTTTTTGAACTTCTAGAGACATAATTGTTGGAACCTCAAAGGATATAGTATGA
Found at i:2019290 original size:333 final size:332
Alignment explanation
Indices: 2018684--2019348 Score: 1186
Period size: 333 Copynumber: 2.0 Consensus size: 332
2018674 GATTACCGCT
2018684 TGATGTAAGGTAATTCTACCTTCTCATTTGATTGTGGATCTAGAAAGGAAGCAAAACAACCTGCA
1 TGATGTAAGGTAATTCTACCTTCTCATTTGATTGTGGATCTAGAAAGGAAGCAAAACAACCTGCA
* * *
2018749 CAAGTGAATGGCTCAAACCAGAATGGATAAGGGTGGTAAACTTATGGTTTAATTGGTAGGCTATT
66 CAAGTGAATGGCTCAAAACAGAATGGATAAGGGTGGTAAACGTATGGTTTAATAGGTAGGCTATT
* *
2018814 TAATAAATGAGAGATGGAAGCGGAAGATGATTGAAATGGTTATGGTTATGGTGATGAAACAAAAG
131 TAATAAATGAGAGATGGAAGCGAAAGATGATTGAAATGGTTATGGTTATGGCGATGAAACAAAAG
* *
2018879 GATGGTTTTGAGGATAGTATCTTGAAGGACGCTCAAAGAAGAACCAATGCTATAGAGAGAAAACA
196 GATGGTTGTGAGGATAGTATCTTGAAGAACGCTCAAAGAAGAACCAATGCTATAGAGAGAAAACA
2018944 CCCAATCTTTATATTGTTTCTTCAAGGGGTGGTGTTAAGTACTTTAACCCACTAGTTATATGAAA
261 CCCAATCTTTATATT-TTTCTTCAAGGGGTGGTGTTAAGTACTTTAACCCACTAGTTATATGAAA
2019009 TAGGAACC
325 TAGGAACC
** *
2019017 TGATGTAAGGTAATTCTACCTTCTTGTTTGATTGTGGATCTAGGAAGGAAGCAAAACAACCTGCA
1 TGATGTAAGGTAATTCTACCTTCTCATTTGATTGTGGATCTAGAAAGGAAGCAAAACAACCTGCA
2019082 CAAGTGAATGGCTCAAAACAGAATGGATAAGGGTGGTAAACGTATGGTTTAATAGGTAGGCTATT
66 CAAGTGAATGGCTCAAAACAGAATGGATAAGGGTGGTAAACGTATGGTTTAATAGGTAGGCTATT
*
2019147 TAATAAATGAGAGATGGAAGCGAAAGATGATTGAAATGGTTATGGTTATGGCGATGAAATAAAAG
131 TAATAAATGAGAGATGGAAGCGAAAGATGATTGAAATGGTTATGGTTATGGCGATGAAACAAAAG
* *
2019212 GATGGTTGTGAGGATAGTATCTTGAAGAACGCTCAAAGAAGAACCAATGCTATAGAGAGCAAAGA
196 GATGGTTGTGAGGATAGTATCTTGAAGAACGCTCAAAGAAGAACCAATGCTATAGAGAGAAAACA
* *
2019277 CCCAATCTTTATATTTTTCTTCAAGGGGTGGTGTTAAGTACTTTGACCCACTAGTTATATGAACT
261 CCCAATCTTTATATTTTTCTTCAAGGGGTGGTGTTAAGTACTTTAACCCACTAGTTATATGAAAT
2019342 AGGAACC
326 AGGAACC
2019349 AGAAGTATCA
Statistics
Matches: 317, Mismatches: 15, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
332 55 0.17
333 262 0.83
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (332 bp):
TGATGTAAGGTAATTCTACCTTCTCATTTGATTGTGGATCTAGAAAGGAAGCAAAACAACCTGCA
CAAGTGAATGGCTCAAAACAGAATGGATAAGGGTGGTAAACGTATGGTTTAATAGGTAGGCTATT
TAATAAATGAGAGATGGAAGCGAAAGATGATTGAAATGGTTATGGTTATGGCGATGAAACAAAAG
GATGGTTGTGAGGATAGTATCTTGAAGAACGCTCAAAGAAGAACCAATGCTATAGAGAGAAAACA
CCCAATCTTTATATTTTTCTTCAAGGGGTGGTGTTAAGTACTTTAACCCACTAGTTATATGAAAT
AGGAACC
Found at i:2023227 original size:23 final size:22
Alignment explanation
Indices: 2023199--2023259 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 22
2023189 CAACTTTTCT
2023199 TTCTTTCTTTTCTTCTTTTCGAG
1 TTCTTTCTTTTCTTCTTTT-GAG
*
2023222 TTCTTTCAATTTCTTCTTTTGAG
1 TTCTTTC-TTTTCTTCTTTTGAG
*
2023245 TTCTTTGATTTTCTT
1 TTCTTT-CTTTTCTT
2023260 TGCTGGATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 22 0.67
24 11 0.33
ACGTcount: A:0.08, C:0.18, G:0.08, T:0.66
Consensus pattern (22 bp):
TTCTTTCTTTTCTTCTTTTGAG
Found at i:2030366 original size:45 final size:45
Alignment explanation
Indices: 2030264--2030364 Score: 145
Period size: 42 Copynumber: 2.3 Consensus size: 45
2030254 AGGATCAGAT
* * *
2030264 TTATTATTTTATTAGGAATTAAGGGTTAAACAATATTTTTAGTTA
1 TTATTATTTTATTAGGAATTAAGAGTTAAACAACATGTTTAGTTA
2030309 TTATTATTTTATTAGGAATT-AGAGTT-AA-AACATGTTTAGTTA
1 TTATTATTTTATTAGGAATTAAGAGTTAAACAACATGTTTAGTTA
*
2030351 TTAATATTTTATTA
1 TTATTATTTTATTA
2030365 TTTAGTTATT
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
42 25 0.48
43 2 0.04
44 5 0.10
45 20 0.38
ACGTcount: A:0.36, C:0.02, G:0.12, T:0.50
Consensus pattern (45 bp):
TTATTATTTTATTAGGAATTAAGAGTTAAACAACATGTTTAGTTA
Found at i:2033333 original size:1 final size:1
Alignment explanation
Indices: 2033329--2033380 Score: 59
Period size: 1 Copynumber: 52.0 Consensus size: 1
2033319 AATTTTGGCA
*** * *
2033329 TTTTTTTTTTTTTTTTTTGCCTTTCTTTTTTTTTTTTTTTTTTTCTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2033381 GAAAAAAAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.00, C:0.08, G:0.02, T:0.90
Consensus pattern (1 bp):
T
Found at i:2033345 original size:21 final size:22
Alignment explanation
Indices: 2033321--2033367 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
2033311 TTTTTTGAAA
2033321 TTTTGGCATTT-TTTTTTTTTT
1 TTTTGGCATTTCTTTTTTTTTT
* *
2033342 TTTTTGCCTTTCTTTTTTTTTT
1 TTTTGGCATTTCTTTTTTTTTT
2033364 TTTT
1 TTTT
2033368 TTTTTCTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.02, C:0.09, G:0.06, T:0.83
Consensus pattern (22 bp):
TTTTGGCATTTCTTTTTTTTTT
Found at i:2033346 original size:22 final size:23
Alignment explanation
Indices: 2033321--2033369 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
2033311 TTTTTTGAAA
*
2033321 TTTTGGCATT-TTTTTTTTTTTT
1 TTTTGCCATTCTTTTTTTTTTTT
*
2033343 TTTTGCCTTTCTTTTTTTTTTTT
1 TTTTGCCATTCTTTTTTTTTTTT
2033366 TTTT
1 TTTT
2033370 TTTCTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 8 0.33
23 16 0.67
ACGTcount: A:0.02, C:0.08, G:0.06, T:0.84
Consensus pattern (23 bp):
TTTTGCCATTCTTTTTTTTTTTT
Found at i:2033373 original size:20 final size:21
Alignment explanation
Indices: 2033331--2033380 Score: 75
Period size: 23 Copynumber: 2.3 Consensus size: 21
2033321 TTTTGGCATT
2033331 TTTTTTTTTTTTTTTTGCCTTTC
1 TTTTTTTTTTTTTTTT--CTTTC
2033354 TTTTTTTTTTTTTTTT-TTTC
1 TTTTTTTTTTTTTTTTCTTTC
2033374 TTTTTTT
1 TTTTTTT
2033381 GAAAAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.41
23 16 0.59
ACGTcount: A:0.00, C:0.08, G:0.02, T:0.90
Consensus pattern (21 bp):
TTTTTTTTTTTTTTTTCTTTC
Found at i:2033638 original size:62 final size:63
Alignment explanation
Indices: 2033557--2033682 Score: 236
Period size: 62 Copynumber: 2.0 Consensus size: 63
2033547 ATCTGATACC
*
2033557 AATTGATAGGGAAGCGGTGGCGGATTGATGAATGTTGCTCTTGTTGAAGAATCAAACCTAGAA
1 AATTGATAGGGAAGCGGTGGCGGATTGATGAACGTTGCTCTTGTTGAAGAATCAAACCTAGAA
2033620 AATT-ATAGGGAAGCGGTGGCGGATTGATGAACGTTGCTCTTGTTGAAGAATCAAACCTAGAA
1 AATTGATAGGGAAGCGGTGGCGGATTGATGAACGTTGCTCTTGTTGAAGAATCAAACCTAGAA
2033682 A
1 A
2033683 GCTCTAGACT
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
62 58 0.94
63 4 0.06
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.26
Consensus pattern (63 bp):
AATTGATAGGGAAGCGGTGGCGGATTGATGAACGTTGCTCTTGTTGAAGAATCAAACCTAGAA
Found at i:2038121 original size:23 final size:22
Alignment explanation
Indices: 2038081--2038138 Score: 84
Period size: 23 Copynumber: 2.7 Consensus size: 22
2038071 TTTTTTGAAA
*
2038081 TTTTGGCTTTTTTTTGTTTTTT
1 TTTTGCCTTTTTTTTGTTTTTT
2038103 TTTTGCCTTTGTTTTTGTTTTTT
1 TTTTGCCTTT-TTTTTGTTTTTT
2038126 TTTTG--TTTTTTTT
1 TTTTGCCTTTTTTTT
2038139 AAAAAATAGC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
20 5 0.15
21 3 0.09
22 9 0.26
23 17 0.50
ACGTcount: A:0.00, C:0.05, G:0.12, T:0.83
Consensus pattern (22 bp):
TTTTGCCTTTTTTTTGTTTTTT
Found at i:2041362 original size:23 final size:24
Alignment explanation
Indices: 2041303--2041362 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
2041293 ACTTTTCTTT
* *
2041303 CTTTCTTTTTCTTCTTTTCGAGTG
1 CTTTCATTTTCTTCCTTTCGAGTG
* *
2041327 CTTTCAATATCTTCCTTT-GAGTG
1 CTTTCATTTTCTTCCTTTCGAGTG
*
2041350 CTTTGATTTTCTT
1 CTTTCATTTTCTT
2041363 TGCTGGATTT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
23 15 0.52
24 14 0.48
ACGTcount: A:0.10, C:0.20, G:0.12, T:0.58
Consensus pattern (24 bp):
CTTTCATTTTCTTCCTTTCGAGTG
Found at i:2048763 original size:12 final size:12
Alignment explanation
Indices: 2048731--2048757 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2048721 CTTGCTTTCT
2048731 TTCACTTTGCAC
1 TTCACTTTGCAC
2048743 TTCACTTTGCAC
1 TTCACTTTGCAC
2048755 TTC
1 TTC
2048758 TTTTTGTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.33, G:0.07, T:0.44
Consensus pattern (12 bp):
TTCACTTTGCAC
Found at i:2051014 original size:350 final size:349
Alignment explanation
Indices: 2050347--2051046 Score: 1179
Period size: 350 Copynumber: 2.0 Consensus size: 349
2050337 TATGCTTATA
2050347 ACATTGTGTATCAATCATAAAGATAGGGTATATGTTGTATGCATGAATATCATATAACATGGTAT
1 ACATTGTGTATCAATCATAAAGATAGGGTATATGTTGTATGCATGAATATCATATAACATGGTAT
* *
2050412 TCATAAATGATAAATGGAAACATGTAATAATAATGTCCTAAGAAATGATATGTAATCATAGCCTA
66 TCATAAATGATAAATGGAAACATGTAATAATAATATCCTAAGAAATGATATGTAATCATAGCATA
* *
2050477 TATTTGAATAATATGAAAAACATGATCAAATAAGCATAGGACGAAAATAATAATATGATAATTTA
131 TATTTGAATAACATGAAAAACATGATCAAATAAGCATAGGACGAAAATAATAATATGATAACTTA
* *
2050542 TACTAACATGTGAATGCATGCTTATGATAGAATATAATGTATAAATGATATAGTATAAGATAGGG
196 TACTAACATGTGAATGCATGCTTATGATAGAATAGAATGTATAAATGATATAATATAAGATAGGG
* *
2050607 TAATGAAGAACTCCCTTAGAAACAGCTATGAAGAACATCCATGGTGTGTTCAAGTCATGGAGAAA
261 TAATGAAGAACTCCCTTAGAAACAGCAATGAAAAACATCCATGGTGTGTTCAAGTCATGGAGAAA
** * *
2050672 GTTGGTGCTTGTTTGGATCGTATC
326 AATGGAGCTAGTTTGGATCGTATC
*
2050696 ACATTGTGTATCAATCATAAAGATGTGGGTATATGTTGTATGCATGAATATCATATAACATGGTA
1 ACATTGTGTATCAATCATAAAGAT-AGGGTATATGTTGTATGCATGAATATCATATAACATGGTA
2050761 TTCATAAATGATAAATGGAAACATGTAATAATAATATCCTAAGAAATGATATGTAATCATAGCAT
65 TTCATAAATGATAAATGGAAACATGTAATAATAATATCCTAAGAAATGATATGTAATCATAGCAT
* * * * *
2050826 ATATTTGAATGACATGAAAGACTTGATCAACTAAGCATAGGATGAAAATAATAATATGATAACTT
130 ATATTTGAATAACATGAAAAACATGATCAAATAAGCATAGGACGAAAATAATAATATGATAACTT
2050891 ATACTAACATGTGAATGCATGCTTATGATAGAATAGAATGTATAAATGATATAATATAAGATAGG
195 ATACTAACATGTGAATGCATGCTTATGATAGAATAGAATGTATAAATGATATAATATAAGATAGG
* *
2050956 GTAA-GAAAGAACTCCCTTAGAATCAGCAATGAAAAACATCCATGGTGT-TATTAAGTCATGGAG
260 GTAATG-AAGAACTCCCTTAGAAACAGCAATGAAAAACATCCATGGTGTGT-TCAAGTCATGGAG
2051019 AAAAATGGAGCTAGTTTGGATCGTATC
323 AAAAATGGAGCTAGTTTGGATCGTATC
2051046 A
1 A
2051047 TCCTCCCCTT
Statistics
Matches: 328, Mismatches: 20, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
349 26 0.08
350 302 0.92
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.30
Consensus pattern (349 bp):
ACATTGTGTATCAATCATAAAGATAGGGTATATGTTGTATGCATGAATATCATATAACATGGTAT
TCATAAATGATAAATGGAAACATGTAATAATAATATCCTAAGAAATGATATGTAATCATAGCATA
TATTTGAATAACATGAAAAACATGATCAAATAAGCATAGGACGAAAATAATAATATGATAACTTA
TACTAACATGTGAATGCATGCTTATGATAGAATAGAATGTATAAATGATATAATATAAGATAGGG
TAATGAAGAACTCCCTTAGAAACAGCAATGAAAAACATCCATGGTGTGTTCAAGTCATGGAGAAA
AATGGAGCTAGTTTGGATCGTATC
Found at i:2056580 original size:19 final size:21
Alignment explanation
Indices: 2056537--2056588 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
2056527 GAAACCCCTT
*
2056537 TGAAAATATATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
2056558 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
2056577 TGAAGATACATG
1 TGAAAATACATG
2056589 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.45
20 4 0.14
21 12 0.41
ACGTcount: A:0.46, C:0.04, G:0.13, T:0.37
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:2059790 original size:336 final size:333
Alignment explanation
Indices: 2059181--2059849 Score: 1232
Period size: 336 Copynumber: 2.0 Consensus size: 333
2059171 GATTACTGCT
*
2059181 TGATGTAAGGTAATTCTACCTTCTCATTTGATTGTGGATCTAGGAAGGAAGTAAAATAACCTGCA
1 TGATGTAAGGTAATTCTACCTTCTCATTTGATTGTGGATCTAGGAAGGAAGTAAAACAACCTGCA
*
2059246 CAAGTGAATGGCTCAAAACAGAATGGATAAGGGTGGTAAACGTATGGTTTAATTGGTAGGCTATT
66 CAAGTGAATGGCTCAAAACAGAATGGATAAGGGTGGTAAACGTATGGTTTAATAGGTAGGCTATT
* *
2059311 TAATAAATGAGAGATGGAAGCGGAAGATGATTGAAATGGTTATGGTTATGGCGATGAAACAAAAG
131 TAATAAATGAGAGATGGAAGCAGAACATGATTGAAATGGTTATGGTTATGGCGATGAAACAAAAG
2059376 GATGGTTGTGAGGATAGTATCTTGAAGAACGCTCAAAGAAGAACCAATGCTATAGAGAGCAAAGA
196 GATGGTTGTGAGGATAGTATCTTGAAGAACGCTCAAAGAAGAACCAATGCTATAGAGAGCAAAGA
2059441 CCCAATCTTTATATTGTTTCTTCAAGGGGTGGTGTTAAGTACTTTGACCCACTAG-TATATGAAC
261 CCCAATCTTTATATTGTTTCTTCAAGGGGTGGTGTTAAGTACTTTGACCCACTAGTTATATGAAC
2059505 TAGGAACC
326 TAGGAACC
**
2059513 TGATGTAAGGTAATTCTACCTTCTTGTTTGATTGTGGATCTAGGAAGGAAGTAAAACAACCTGCA
1 TGATGTAAGGTAATTCTACCTTCTCATTTGATTGTGGATCTAGGAAGGAAGTAAAACAACCTGCA
*
2059578 CAAGTGAATGGCTCAAAACATAATGGATAAGGGTGGTAAACGTATGGTTTAATAGGTAGGCTATT
66 CAAGTGAATGGCTCAAAACAGAATGGATAAGGGTGGTAAACGTATGGTTTAATAGGTAGGCTA-T
2059643 TAATAAATAAATGAGAGATGGAAGCAGAACATGATTGAAATGGTTATGGTTATGGCGATGAAACA
130 T--T-AATAAATGAGAGATGGAAGCAGAACATGATTGAAATGGTTATGGTTATGGCGATGAAACA
2059708 AAAGGATGGTTGTGAGGATAGTATCTTGAAGAACGCTCAAAGAAGAACCAATGCTATAGAGAGCA
192 AAAGGATGGTTGTGAGGATAGTATCTTGAAGAACGCTCAAAGAAGAACCAATGCTATAGAGAGCA
2059773 AAGACCCAATCTTTATATTGTTTCTTCAAGGGGTGGTGTTAAGTACTTTGACCCACTAGTTATAT
257 AAGACCCAATCTTTATATTGTTTCTTCAAGGGGTGGTGTTAAGTACTTTGACCCACTAGTTATAT
2059838 GAACTAGGAACC
322 GAACTAGGAACC
2059850 AGAAGTATCA
Statistics
Matches: 325, Mismatches: 7, Indels: 5
0.96 0.02 0.01
Matches are distributed among these distances:
332 123 0.38
333 2 0.01
335 1 0.00
336 182 0.56
337 17 0.05
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (333 bp):
TGATGTAAGGTAATTCTACCTTCTCATTTGATTGTGGATCTAGGAAGGAAGTAAAACAACCTGCA
CAAGTGAATGGCTCAAAACAGAATGGATAAGGGTGGTAAACGTATGGTTTAATAGGTAGGCTATT
TAATAAATGAGAGATGGAAGCAGAACATGATTGAAATGGTTATGGTTATGGCGATGAAACAAAAG
GATGGTTGTGAGGATAGTATCTTGAAGAACGCTCAAAGAAGAACCAATGCTATAGAGAGCAAAGA
CCCAATCTTTATATTGTTTCTTCAAGGGGTGGTGTTAAGTACTTTGACCCACTAGTTATATGAAC
TAGGAACC
Found at i:2063757 original size:23 final size:24
Alignment explanation
Indices: 2063715--2063767 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
2063705 CTTTATTTTT
2063715 TTTCTTCTTTTCGAGTGCTTTCAA
1 TTTCTTCTTTTCGAGTGCTTTCAA
* *
2063739 TTTCTTCTTTT-GAGTGCTTTGAT
1 TTTCTTCTTTTCGAGTGCTTTCAA
2063762 TTTCTT
1 TTTCTT
2063768 TGCTGGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.09, C:0.17, G:0.13, T:0.60
Consensus pattern (24 bp):
TTTCTTCTTTTCGAGTGCTTTCAA
Found at i:2070303 original size:15 final size:17
Alignment explanation
Indices: 2070267--2070300 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
2070257 TTTGATAACA
2070267 TTTC-TATCTATTTCCT
1 TTTCTTATCTATTTCCT
2070283 TTTCTTATC-ATTTCCT
1 TTTCTTATCTATTTCCT
2070299 TT
1 TT
2070301 CTTCTTTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.12, C:0.24, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTCTTATCTATTTCCT
Found at i:2079227 original size:21 final size:20
Alignment explanation
Indices: 2079191--2079246 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
2079181 GGAGTGCAAA
*
2079191 AAGAAAAGAC-AAAAAGAAG
1 AAGAAAAGTCAAAAAAGAAG
*
2079210 AAGAAAAATTCAAAAAAGAAG
1 AAG-AAAAGTCAAAAAAGAAG
2079231 AAGAAAAGTCAAAAAA
1 AAGAAAAGTCAAAAAA
2079247 AGAGAAAGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.09
20 17 0.53
21 12 0.38
ACGTcount: A:0.73, C:0.05, G:0.16, T:0.05
Consensus pattern (20 bp):
AAGAAAAGTCAAAAAAGAAG
Found at i:2079249 original size:18 final size:19
Alignment explanation
Indices: 2079191--2079253 Score: 76
Period size: 21 Copynumber: 3.3 Consensus size: 19
2079181 GGAGTGCAAA
*
2079191 AAGAAAAGACAAAAAGAAG
1 AAGAAAAGTCAAAAAGAAG
*
2079210 AAGAAAAATTCAAAAAAGAAG
1 AAG-AAAAGTC-AAAAAGAAG
2079231 AAGAAAAGTCAAAAA-AAG
1 AAGAAAAGTCAAAAAGAAG
2079249 -AGAAA
1 AAGAAA
2079254 GCAAGCCAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
17 5 0.13
18 3 0.08
19 8 0.21
20 11 0.28
21 12 0.31
ACGTcount: A:0.73, C:0.05, G:0.17, T:0.05
Consensus pattern (19 bp):
AAGAAAAGTCAAAAAGAAG
Found at i:2086298 original size:21 final size:24
Alignment explanation
Indices: 2086254--2086299 Score: 62
Period size: 21 Copynumber: 2.0 Consensus size: 24
2086244 GGTTGAAGAT
2086254 GATTATTTTAACTTTGAACGTGCA
1 GATTATTTTAACTTTGAACGTGCA
*
2086278 GATT-TTTT-ACTTT-AACTTGCA
1 GATTATTTTAACTTTGAACGTGCA
2086299 G
1 G
2086300 GATGTACCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 8 0.38
22 5 0.24
23 4 0.19
24 4 0.19
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.46
Consensus pattern (24 bp):
GATTATTTTAACTTTGAACGTGCA
Found at i:2086818 original size:13 final size:13
Alignment explanation
Indices: 2086800--2086833 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
2086790 GATGATGGTC
2086800 TTGATGAAGGATG
1 TTGATGAAGGATG
*
2086813 TTGATGATGGATG
1 TTGATGAAGGATG
*
2086826 ATGATGAA
1 TTGATGAA
2086834 ATGGCAATGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.35, T:0.32
Consensus pattern (13 bp):
TTGATGAAGGATG
Found at i:2087225 original size:19 final size:20
Alignment explanation
Indices: 2087186--2087234 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
2087176 AACCCCTTTT
**
2087186 AAAATACATGAATTTTGATG
1 AAAATACATGAATTTAAATG
2087206 AAAATACATG-ATTTAAATG
1 AAAATACATGAATTTAAATG
*
2087225 AAGATACATG
1 AAAATACATG
2087235 CTCTTGGTCG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.49, C:0.06, G:0.14, T:0.31
Consensus pattern (20 bp):
AAAATACATGAATTTAAATG
Found at i:2092293 original size:13 final size:11
Alignment explanation
Indices: 2092252--2092336 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
2092242 ACAATCTGTC
2092252 CATCACCATTAT
1 CATCACCA-TAT
*
2092264 CA-CGCCTATAT
1 CATCACC-ATAT
2092275 CATCACCATAGT
1 CATCACCATA-T
2092287 CCATCACCATTAT
1 -CATCACCA-TAT
*
2092300 CA-CGCCTATAT
1 CATCACC-ATAT
2092311 CATCACCATATT
1 CATCACCATA-T
2092323 CCATCACCATAT
1 -CATCACCATAT
2092335 CA
1 CA
2092337 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:2092296 original size:36 final size:36
Alignment explanation
Indices: 2092249--2092353 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
2092239 GATACAATCT
2092249 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
2092285 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
2092321 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
2092354 ACTTATAAAT
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 21 0.31
36 46 0.69
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:2092556 original size:19 final size:19
Alignment explanation
Indices: 2092532--2092570 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
2092522 TCCTTTCTTA
2092532 ATTACTCATTTACTTAACC
1 ATTACTCATTTACTTAACC
2092551 ATTACTCATTTACTTAACC
1 ATTACTCATTTACTTAACC
2092570 A
1 A
2092571 ATCATTCTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.26, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTACTCATTTACTTAACC
Found at i:2095212 original size:19 final size:20
Alignment explanation
Indices: 2095165--2095215 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
2095155 GAAACCCCTT
**
2095165 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
2095185 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
2095204 TGAAGATACATG
1 TGAAAATACATG
2095216 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:2098845 original size:24 final size:24
Alignment explanation
Indices: 2098816--2098877 Score: 88
Period size: 27 Copynumber: 2.5 Consensus size: 24
2098806 CTAGTGACCT
2098816 CTTTTTCTTTTGCCTCTTTCTTAA
1 CTTTTTCTTTTGCCTCTTTCTTAA
*
2098840 CTTTTTCTTTTTTTGCCTCTTTCTTAG
1 CTTTTTC---TTTTGCCTCTTTCTTAA
2098867 CTTTTTCTTTT
1 CTTTTTCTTTT
2098878 TTTGCTTTCC
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
24 11 0.32
27 23 0.68
ACGTcount: A:0.05, C:0.23, G:0.05, T:0.68
Consensus pattern (24 bp):
CTTTTTCTTTTGCCTCTTTCTTAA
Found at i:2098860 original size:27 final size:27
Alignment explanation
Indices: 2098823--2098882 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
2098813 CCTCTTTTTC
2098823 TTTTGCCTCTTTCTTAACTTTTTCTTT
1 TTTTGCCTCTTTCTTAACTTTTTCTTT
*
2098850 TTTTGCCTCTTTCTTAGCTTTTTCTTT
1 TTTTGCCTCTTTCTTAACTTTTTCTTT
2098877 TTTTGC
1 TTTTGC
2098883 TTTCCCTACC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.05, C:0.22, G:0.07, T:0.67
Consensus pattern (27 bp):
TTTTGCCTCTTTCTTAACTTTTTCTTT
Found at i:2100144 original size:33 final size:33
Alignment explanation
Indices: 2100102--2100170 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
2100092 GTTGATGAAT
*
2100102 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
2100135 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
2100168 GAA
1 GAA
2100171 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:2100175 original size:13 final size:12
Alignment explanation
Indices: 2100156--2100241 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
2100146 TTATTGGCGT
2100156 GATATGGTGATG
1 GATATGGTGATG
2100168 GAATATGGTGAT-
1 G-ATATGGTGATG
*
2100180 GATATAGGCG-T-
1 GATAT-GGTGATG
2100191 GATAATGGTGATG
1 GAT-ATGGTGATG
2100204 GACTATGGTGAT-
1 GA-TATGGTGATG
*
2100216 GATATAGGCG-T-
1 GATAT-GGTGATG
2100227 GATAATGGTGATG
1 GAT-ATGGTGATG
2100240 GA
1 GA
2100242 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:2100211 original size:36 final size:36
Alignment explanation
Indices: 2100141--2100242 Score: 170
Period size: 36 Copynumber: 2.9 Consensus size: 36
2100131 AATGGAAGGA
* * *
2100141 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
2100176 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
2100212 TGATGATATAGGCGTGATAATGGTGATGGAC
1 TGATGATATAGGCGTGATAATGGTGATGGAC
2100243 AGATTGTATC
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 16 0.25
36 47 0.75
ACGTcount: A:0.26, C:0.05, G:0.36, T:0.32
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGACTATGG
Found at i:2104006 original size:23 final size:24
Alignment explanation
Indices: 2103963--2104011 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
2103953 AAAGATTAAG
*
2103963 AAAGATGATAAGGTAATGAAAAGA
1 AAAGATGATAAGATAATGAAAAGA
*
2103987 AAAGATGA-AAGAATAA-GAAATGA
1 AAAGATGATAAG-ATAATGAAAAGA
2104010 AA
1 AA
2104012 TAGTAAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.63, C:0.00, G:0.22, T:0.14
Consensus pattern (24 bp):
AAAGATGATAAGATAATGAAAAGA
Found at i:2104654 original size:33 final size:33
Alignment explanation
Indices: 2104612--2104680 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
2104602 GTTGATGAAT
*
2104612 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* *
2104645 GAAGGATGATGTTATTGGCGTGATATGGTAATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
2104678 GAA
1 GAA
2104681 TATGGTGATG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 25 0.78
34 7 0.22
ACGTcount: A:0.33, C:0.01, G:0.35, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:2104725 original size:36 final size:36
Alignment explanation
Indices: 2104651--2104752 Score: 143
Period size: 36 Copynumber: 2.9 Consensus size: 36
2104641 AATGGAAGGA
* * * *
2104651 TGATGTTATTGGCGTGAT-ATGGTAATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATCG
* *
2104686 TGATGATGTAGGCGTGATAATGGTGATGGACTATCG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATCG
2104722 TGATGATATAGGCGTGATAATGGTGATGGAA
1 TGATGATATAGGCGTGATAATGGTGATGGAA
2104753 AGATTGTATC
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
35 15 0.26
36 43 0.74
ACGTcount: A:0.27, C:0.05, G:0.35, T:0.32
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATCG
Found at i:2106706 original size:11 final size:11
Alignment explanation
Indices: 2106692--2106716 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2106682 AAATTTTGGC
2106692 TTTTTTGTTTT
1 TTTTTTGTTTT
2106703 TTTTTTGTTTT
1 TTTTTTGTTTT
2106714 TTT
1 TTT
2106717 AAAAAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (11 bp):
TTTTTTGTTTT
Found at i:2111083 original size:15 final size:16
Alignment explanation
Indices: 2111063--2111099 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
2111053 TCTTTGATAA
2111063 CATTTCTATCCA-TTT
1 CATTTCTATCCATTTT
*
2111078 CATTTCTTTCCATTTT
1 CATTTCTATCCATTTT
2111094 CATTTC
1 CATTTC
2111100 CTTTCTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.16, C:0.27, G:0.00, T:0.57
Consensus pattern (16 bp):
CATTTCTATCCATTTT
Found at i:2119182 original size:25 final size:25
Alignment explanation
Indices: 2119148--2119198 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
2119138 TCTCTCAATG
2119148 TTGTGTCAAATTTGTTCATGTAACT
1 TTGTGTCAAATTTGTTCATGTAACT
2119173 TTGTGTCAAATTTGTTCATGTAACT
1 TTGTGTCAAATTTGTTCATGTAACT
2119198 T
1 T
2119199 CTTAATGAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.24, C:0.12, G:0.16, T:0.49
Consensus pattern (25 bp):
TTGTGTCAAATTTGTTCATGTAACT
Found at i:2124921 original size:11 final size:13
Alignment explanation
Indices: 2124889--2124918 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2124879 TGGCCAAAGA
2124889 TGAAAAGGTATGT
1 TGAAAAGGTATGT
2124902 TGAAAAGGTATG-
1 TGAAAAGGTATGT
2124914 TGAAA
1 TGAAA
2124919 GGTGTTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:2126299 original size:269 final size:269
Alignment explanation
Indices: 2125820--2126358 Score: 988
Period size: 269 Copynumber: 2.0 Consensus size: 269
2125810 TTCAACATCA
* *
2125820 CTGATACTATCCAAACAAGCTCCAACTTTCTCCATGACTTGAACACACCATGGATGTTCTTCATA
1 CTGATACGATCCAAACAAGCTCCAACTTTCTCCATGACTTGAACACACCATGGATGTTCTTCAAA
2125885 GCTGTTTCTAAGGGAGTTCTTCATTACCCTATCTTATACTATATCATTTATACATTATATTCTAT
66 GCTGTTTCTAAGGGAGTTCTTCATTACCCTATCTTATACTATATCATTTATACATTATATTCTAT
* *
2125950 CATAAGCATGCATTCACATGTTAGTATAAATTATCATATTATTATTTTCATCCTATGCTTATTTG
131 CAAAAGCATGCATTCACATGTTAGTATAAATTATCATATTATTATTTCCATCCTATGCTTATTTG
*
2126015 ATCATGTTTTTCATATTATTCAAATATATGCTATGATTACATATCATTTCTTAGGACATTATTAT
196 ATCATGTTTTTCATATTATTCAAATATATGCTATAATTACATATCATTTCTTAGGACATTATTAT
2126080 TACATGTTT
261 TACATGTTT
*
2126089 CTGATACGATCCAAACTAGCTCCAACTTTCTCCATGACTTGAACACACCATGGATGTTCTTCAAA
1 CTGATACGATCCAAACAAGCTCCAACTTTCTCCATGACTTGAACACACCATGGATGTTCTTCAAA
* *
2126154 GTTGTTTCTAAGGGAGTTCTTCATTACCCTATCTTATACTATATCATTTATACATTCTATTCTAT
66 GCTGTTTCTAAGGGAGTTCTTCATTACCCTATCTTATACTATATCATTTATACATTATATTCTAT
*
2126219 CAAAAGCATGCATTCATATGTTAGTATAAATTATCATATTATTATTTCCATCCTATGCTTATTTG
131 CAAAAGCATGCATTCACATGTTAGTATAAATTATCATATTATTATTTCCATCCTATGCTTATTTG
*
2126284 ATCATGTTTTTCATATTATTCAAATATATGCTATAATTACATATCATTTCTTAGGATATTATTAT
196 ATCATGTTTTTCATATTATTCAAATATATGCTATAATTACATATCATTTCTTAGGACATTATTAT
2126349 TACATGTTT
261 TACATGTTT
2126358 C
1 C
2126359 CATTTATCAT
Statistics
Matches: 260, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
269 260 1.00
ACGTcount: A:0.30, C:0.19, G:0.09, T:0.42
Consensus pattern (269 bp):
CTGATACGATCCAAACAAGCTCCAACTTTCTCCATGACTTGAACACACCATGGATGTTCTTCAAA
GCTGTTTCTAAGGGAGTTCTTCATTACCCTATCTTATACTATATCATTTATACATTATATTCTAT
CAAAAGCATGCATTCACATGTTAGTATAAATTATCATATTATTATTTCCATCCTATGCTTATTTG
ATCATGTTTTTCATATTATTCAAATATATGCTATAATTACATATCATTTCTTAGGACATTATTAT
TACATGTTT
Found at i:2127263 original size:90 final size:91
Alignment explanation
Indices: 2127109--2127290 Score: 258
Period size: 90 Copynumber: 2.0 Consensus size: 91
2127099 CCTAGAACAC
*
2127109 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
*
2127174 AAGAGTTCTCTCCCTATTCAGCCAAG
66 AAGAGCTCTCTCCCTATTCAGCCAAG
** * * * * * *
2127200 CCATGTGTTTTGCATGTGAACAG-CCCCATGTTCCTTGCATGTGGTTTATTTAGGTGCCAAGATG
1 CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
*
2127264 AAGAGCTCTCTCCCTATTCGGCCAAG
66 AAGAGCTCTCTCCCTATTCAGCCAAG
2127290 C
1 C
2127291 ATTATTTCCC
Statistics
Matches: 80, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
90 61 0.76
91 19 0.24
ACGTcount: A:0.21, C:0.27, G:0.23, T:0.29
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
AAGAGCTCTCTCCCTATTCAGCCAAG
Found at i:2129401 original size:24 final size:24
Alignment explanation
Indices: 2129374--2129430 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
2129364 GACATGTCCT
*
2129374 TTGACGTTCCAACAATTATGCCAC
1 TTGAAGTTCCAACAATTATGCCAC
2129398 TTGAAGTTCCAACAATTATGCCAC
1 TTGAAGTTCCAACAATTATGCCAC
2129422 TTGAAGTTC
1 TTGAAGTTC
2129431 AAAAAGATGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.32
Consensus pattern (24 bp):
TTGAAGTTCCAACAATTATGCCAC
Found at i:2129465 original size:24 final size:24
Alignment explanation
Indices: 2129395--2129473 Score: 72
Period size: 24 Copynumber: 3.3 Consensus size: 24
2129385 ACAATTATGC
* *
2129395 CACTTGAAGTTCCAACAA-TTATGC
1 CACTTGAAGTTCC-ACAAGTTGTGT
* * *
2129419 CACTTGAAGTTCAAAAAGATGTGT
1 CACTTGAAGTTCCACAAGTTGTGT
*
2129443 CACTTGAAGTGCCACAAGTTGTGAT
1 CACTTGAAGTTCCACAAGTTGTG-T
2129468 CA-TTGA
1 CACTTGA
2129474 GGCTCCAAGT
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
23 3 0.07
24 38 0.86
25 3 0.07
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (24 bp):
CACTTGAAGTTCCACAAGTTGTGT
Found at i:2131144 original size:90 final size:91
Alignment explanation
Indices: 2130999--2131171 Score: 258
Period size: 90 Copynumber: 1.9 Consensus size: 91
2130989 CCCATGTGCC
* * * *
2130999 TTGCATATGACCAGCCCCCTTGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATGAAGAGTTCT
1 TTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCACCAAGATGAAGAGCTCT
2131064 CTCCCTATTCGGCCAAGCCATGTATT
66 CTCCCTATTCGGCCAAGCCATGTATT
* * * * *
2131090 TTGCATGTGAACAG-CCCCATGTGCCTTGTATGTGGTTTATTTAGGCACCAAGATGAAGAGCTCT
1 TTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCACCAAGATGAAGAGCTCT
2131154 CTCCCTATTCGGCCAAGC
66 CTCCCTATTCGGCCAAGC
2131172 ATCATTTCCC
Statistics
Matches: 73, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
90 61 0.84
91 12 0.16
ACGTcount: A:0.22, C:0.27, G:0.23, T:0.29
Consensus pattern (91 bp):
TTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCACCAAGATGAAGAGCTCT
CTCCCTATTCGGCCAAGCCATGTATT
Found at i:2133637 original size:23 final size:22
Alignment explanation
Indices: 2133582--2133638 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
2133572 AATCAGTAAT
*
2133582 GAAAATAAAGGCACTCAAAAGAA
1 GAAAAGAAA-GCACTCAAAAGAA
**
2133605 GCAATTGAAAGCACTCGAAAAGAA
1 G-AAAAGAAAGCACTC-AAAAGAA
2133629 GAAAAGAAAG
1 GAAAAGAAAG
2133639 AAAGAAAAGT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
23 14 0.52
24 13 0.48
ACGTcount: A:0.58, C:0.12, G:0.21, T:0.09
Consensus pattern (22 bp):
GAAAAGAAAGCACTCAAAAGAA
Found at i:2134816 original size:24 final size:24
Alignment explanation
Indices: 2134781--2134831 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
2134771 TCACTTCAAG
* *
2134781 TTGAAGATTCAAGAAACATGTCTT
1 TTGAAGAATCAAGAAACATGACTT
* *
2134805 TTGAAGAATCAATAGACATGACTT
1 TTGAAGAATCAAGAAACATGACTT
2134829 TTG
1 TTG
2134832 GTGATGCACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (24 bp):
TTGAAGAATCAAGAAACATGACTT
Found at i:2134880 original size:24 final size:21
Alignment explanation
Indices: 2134846--2134888 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
2134836 TGCACAAGAT
*
2134846 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
2134868 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
2134889 AGAATGAGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:2141827 original size:24 final size:22
Alignment explanation
Indices: 2141772--2141827 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
2141762 TTTTCTTTGC
*
2141772 TTTTTTCTTTTTGAGTGCTGGAT
1 TTTTTTC-TTTTGAGTGCTGCAT
*
2141795 TTTTCTTCTTTTGAGTGCTTCACT
1 TTTT-TTCTTTTGAGTGCTGCA-T
2141819 TTGTTTTCT
1 TT-TTTTCT
2141828 GATTTTTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
23 16 0.57
24 10 0.36
25 2 0.07
ACGTcount: A:0.07, C:0.14, G:0.16, T:0.62
Consensus pattern (22 bp):
TTTTTTCTTTTGAGTGCTGCAT
Found at i:2144442 original size:24 final size:24
Alignment explanation
Indices: 2144406--2144457 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
2144396 TTGTGGATTA
** *
2144406 TCAAAAGTTATGTCTATTGATTCT
1 TCAAAAGACATGTCTATTGAATCT
* *
2144430 TCAAAAGACATGTTTCTTGAATCT
1 TCAAAAGACATGTCTATTGAATCT
2144454 TCAA
1 TCAA
2144458 CTTGAAGTGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (24 bp):
TCAAAAGACATGTCTATTGAATCT
Found at i:2148900 original size:19 final size:18
Alignment explanation
Indices: 2148848--2148903 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
2148838 AATTGGAGTG
2148848 AAAAAG-AAAGAAAAAGA
1 AAAAAGAAAAGAAAAAGA
*
2148865 CATAAAGAAGAAG-AAAAGA
1 -AAAAAGAA-AAGAAAAAGA
2148884 AGAAAAGAAAAGAAAAAGA
1 A-AAAAGAAAAGAAAAAGA
2148903 A
1 A
2148904 TTCAAAAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
18 9 0.28
19 20 0.62
20 3 0.09
ACGTcount: A:0.77, C:0.02, G:0.20, T:0.02
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAAGA
Found at i:2154371 original size:8 final size:8
Alignment explanation
Indices: 2154360--2154429 Score: 63
Period size: 9 Copynumber: 8.4 Consensus size: 8
2154350 TCTTTTTGAA
2154360 TTTTTCTT
1 TTTTTCTT
2154368 TTTTTCTTT
1 TTTTTC-TT
2154377 TCTTTTCTT
1 T-TTTTCTT
*
2154386 CTTTTC--
1 TTTTTCTT
*
2154392 TTCTTCTT
1 TTTTTCTT
2154400 TTTCTTCTT
1 TTT-TTCTT
2154409 TTTTGTCTT
1 TTTT-TCTT
2154418 TTCTTTCTT
1 TT-TTTCTT
2154427 TTT
1 TTT
2154430 GCACTCCAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
6 4 0.08
8 15 0.29
9 25 0.49
10 7 0.14
ACGTcount: A:0.00, C:0.19, G:0.01, T:0.80
Consensus pattern (8 bp):
TTTTTCTT
Found at i:2154382 original size:18 final size:18
Alignment explanation
Indices: 2154361--2154428 Score: 84
Period size: 18 Copynumber: 3.7 Consensus size: 18
2154351 CTTTTTGAAT
*
2154361 TTTTCTTTTTTTCTTTTC
1 TTTTCTTCTTTTCTTTTC
2154379 TTTTCTTCTTTTCTTCTTC
1 TTTTCTTCTTTTCTT-TTC
*
2154398 TTTTTCTTCTTTT-TTGTC
1 -TTTTCTTCTTTTCTTTTC
2154416 TTTTCTTTCTTTT
1 TTTTC-TTCTTTT
2154429 TGCACTCCAA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
17 5 0.11
18 23 0.51
19 5 0.11
20 12 0.27
ACGTcount: A:0.00, C:0.19, G:0.01, T:0.79
Consensus pattern (18 bp):
TTTTCTTCTTTTCTTTTC
Found at i:2154384 original size:32 final size:31
Alignment explanation
Indices: 2154348--2154419 Score: 74
Period size: 32 Copynumber: 2.3 Consensus size: 31
2154338 CTTAAATTGC
*
2154348 TTTCTTTTTGAATTTTTCTTTTT-TTCTTTTCT
1 TTTCTTTTT-AATTCTTCTTTTTCTTCTTTT-T
**
2154380 TTTCTTCTTTTCTTCTTCTTTTTCTTCTTTTT
1 TTTCTT-TTTAATTCTTCTTTTTCTTCTTTTT
*
2154412 TGTCTTTT
1 TTTCTTTT
2154420 CTTTCTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
31 2 0.06
32 22 0.65
33 10 0.29
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.78
Consensus pattern (31 bp):
TTTCTTTTTAATTCTTCTTTTTCTTCTTTTT
Found at i:2154411 original size:29 final size:30
Alignment explanation
Indices: 2154363--2154429 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 30
2154353 TTTTGAATTT
*
2154363 TTCTT-TTTTTCTTTTCTTTTCT-TCTTTTC
1 TTCTTCTTTTTCTTCTCTTTT-TGTCTTTTC
2154392 TTCTTCTTTTTCTTCT-TTTTTGTCTTTTC
1 TTCTTCTTTTTCTTCTCTTTTTGTCTTTTC
2154421 -T-TTCTTTTT
1 TTCTTCTTTTT
2154430 GCACTCCAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
27 8 0.23
28 2 0.06
29 16 0.46
30 9 0.26
ACGTcount: A:0.00, C:0.19, G:0.01, T:0.79
Consensus pattern (30 bp):
TTCTTCTTTTTCTTCTCTTTTTGTCTTTTC
Found at i:2154424 original size:21 final size:20
Alignment explanation
Indices: 2154363--2154426 Score: 85
Period size: 21 Copynumber: 3.1 Consensus size: 20
2154353 TTTTGAATTT
2154363 TTCTTTTTTTCTTTTCTTTTC
1 TTCTTTTTTTCTTTTC-TTTC
*
2154384 TTCTTTTCTTCTTCTT-TTTC
1 TTCTTTTTTTCTT-TTCTTTC
2154404 TTCTTTTTTGTCTTTTCTTTC
1 TTCTTTTTT-TCTTTTCTTTC
2154425 TT
1 TT
2154427 TTTGCACTCC
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
20 14 0.37
21 22 0.58
22 2 0.05
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (20 bp):
TTCTTTTTTTCTTTTCTTTC
Found at i:2154718 original size:21 final size:21
Alignment explanation
Indices: 2154692--2154734 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
2154682 TTAAGAAATG
2154692 AATAATAAT-ATAAGTAATGAA
1 AATAATAATAATAAG-AATGAA
2154713 AATAATAATAATAAGAATGAA
1 AATAATAATAATAAGAATGAA
2154734 A
1 A
2154735 TGAAATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (21 bp):
AATAATAATAATAAGAATGAA
Found at i:2158587 original size:17 final size:16
Alignment explanation
Indices: 2158547--2158587 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
2158537 CAAAAGCAAC
2158547 AAAAAGAAAAAAAAAG
1 AAAAAGAAAAAAAAAG
*
2158563 AAAGAAGAAAACAAAAG
1 AAA-AAGAAAAAAAAAG
2158580 AGAAAAGA
1 A-AAAAGA
2158588 CTCCTTCAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 3 0.14
17 17 0.77
18 2 0.09
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAAAAAAAG
Found at i:2158634 original size:14 final size:13
Alignment explanation
Indices: 2158617--2158666 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
2158607 GTGCAAAAAG
2158617 AAAGAAAAAGACAA
1 AAAGAAAAAGA-AA
*
2158631 AAAGAAGAAGAAA
1 AAAGAAAAAGAAA
2158644 AGAAG-AAAAG--A
1 A-AAGAAAAAGAAA
2158655 AAAGAAAAAGAA
1 AAAGAAAAAGAA
2158667 TTCAAAAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
10 3 0.10
11 7 0.23
13 7 0.23
14 13 0.43
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:2158663 original size:19 final size:18
Alignment explanation
Indices: 2158611--2158666 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 18
2158601 ATTGGAGTGC
2158611 AAAAAG-AAAGAAAAAGA
1 AAAAAGAAAAGAAAAAGA
2158628 CAAAAAGAAGAAG-AAAAGA
1 -AAAAAGAA-AAGAAAAAGA
2158647 AGAAAAGAAAAGAAAAAGA
1 A-AAAAGAAAAGAAAAAGA
2158666 A
1 A
2158667 TTCAAAAAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 10 0.29
19 21 0.62
20 3 0.09
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAAGA
Found at i:2170519 original size:23 final size:23
Alignment explanation
Indices: 2170466--2170519 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
2170456 TCAATTGGCC
*
2170466 CATTCTTTTGAATTTCAATAGGTA
1 CATTC-TTTGAATTGCAATAGGTA
2170490 CATTCTTTGAAATTGCAA-AGG-A
1 CATTCTTTG-AATTGCAATAGGTA
2170512 CATATCTT
1 CAT-TCTT
2170520 GTGGATCGCC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 4 0.15
23 11 0.41
24 12 0.44
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (23 bp):
CATTCTTTGAATTGCAATAGGTA
Found at i:2171733 original size:5 final size:5
Alignment explanation
Indices: 2171723--2171758 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
2171713 GTGCTTCAAC
2171723 TTTCT TTTCT TTTCT TTTCT TTTC- TTT-T TTTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
2171759 TGAGTGCTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 6 0.21
5 23 0.79
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTCT
Found at i:2171743 original size:15 final size:13
Alignment explanation
Indices: 2171723--2171758 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 13
2171713 GTGCTTCAAC
2171723 TTTCTTTTCTTTTCT
1 TTTCTTTTC-TTT-T
2171738 TTTCTTTTCTTTT
1 TTTCTTTTCTTTT
2171751 TTTCTTTT
1 TTTCTTTT
2171759 TGAGTGCTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 9 0.43
14 3 0.14
15 9 0.43
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTCTTTTCTTTT
Found at i:2180085 original size:10 final size:10
Alignment explanation
Indices: 2180070--2180137 Score: 61
Period size: 10 Copynumber: 6.9 Consensus size: 10
2180060 TATTTGTTCA
2180070 AAAAAAAAAC
1 AAAAAAAAAC
2180080 AAAAAAAAAC
1 AAAAAAAAAC
*
2180090 -AAAAAAAAG
1 AAAAAAAAAC
* **
2180099 GAAAAAAGGC
1 AAAAAAAAAC
2180109 --AAAAAAAC
1 AAAAAAAAAC
2180117 AAACAAAAAAGC
1 AAA-AAAAAA-C
2180129 AAAAAAAAA
1 AAAAAAAAA
2180138 AAGCCAAAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
8 6 0.13
9 8 0.17
10 17 0.36
11 12 0.26
12 4 0.09
ACGTcount: A:0.84, C:0.09, G:0.07, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:2180113 original size:29 final size:29
Alignment explanation
Indices: 2180079--2180134 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
2180069 AAAAAAAAAA
*
2180079 CAAAAAAA-AACAAAAAAAAGGAAAAAAGG
1 CAAAAAAACAA-AAAAAAAAGCAAAAAAGG
*
2180108 CAAAAAAACAAACAAAAAAGCAAAAAA
1 CAAAAAAACAAAAAAAAAAGCAAAAAA
2180135 AAAAAGCCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 22 0.92
30 2 0.08
ACGTcount: A:0.80, C:0.11, G:0.09, T:0.00
Consensus pattern (29 bp):
CAAAAAAACAAAAAAAAAAGCAAAAAAGG
Found at i:2189608 original size:11 final size:11
Alignment explanation
Indices: 2189594--2189653 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
2189584 TTTTTTGAAA
2189594 TTTTGGTTTTT
1 TTTTGGTTTTT
*
2189605 TTTT-GCTTTT
1 TTTTGGTTTTT
*
2189615 TTTTGTTTTTTT
1 TTTTG-GTTTTT
**
2189627 TTTTGCATTTT
1 TTTTGGTTTTT
2189638 TTTT-GTTTTT
1 TTTTGGTTTTT
2189648 TGTTTG
1 T-TTTG
2189654 AAAAAATAGC
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
10 14 0.37
11 15 0.39
12 9 0.24
ACGTcount: A:0.02, C:0.03, G:0.13, T:0.82
Consensus pattern (11 bp):
TTTTGGTTTTT
Found at i:2189626 original size:23 final size:23
Alignment explanation
Indices: 2189600--2189648 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
2189590 GAAATTTTGG
2189600 TTTTTTTTTGC-TTTTTTTTGTT
1 TTTTTTTTTGCATTTTTTTTGTT
2189622 TTTTTTTTTGCATTTTTTTTGTT
1 TTTTTTTTTGCATTTTTTTTGTT
2189645 TTTT
1 TTTT
2189649 GTTTGAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 11 0.42
23 15 0.58
ACGTcount: A:0.02, C:0.04, G:0.08, T:0.86
Consensus pattern (23 bp):
TTTTTTTTTGCATTTTTTTTGTT
Found at i:2189627 original size:9 final size:10
Alignment explanation
Indices: 2189601--2189648 Score: 53
Period size: 10 Copynumber: 4.6 Consensus size: 10
2189591 AAATTTTGGT
2189601 TTTTTTTTGC
1 TTTTTTTTGC
*
2189611 TTTTTTTTGTTT
1 TTTTTTTTG--C
2189623 TTTTTTTTGC
1 TTTTTTTTGC
2189633 ATTTTTTTTG-
1 -TTTTTTTTGC
2189643 TTTTTT
1 TTTTTT
2189649 GTTTGAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
9 6 0.18
10 9 0.27
11 9 0.27
12 9 0.27
ACGTcount: A:0.02, C:0.04, G:0.08, T:0.85
Consensus pattern (10 bp):
TTTTTTTTGC
Found at i:2189653 original size:22 final size:20
Alignment explanation
Indices: 2189594--2189653 Score: 75
Period size: 22 Copynumber: 2.8 Consensus size: 20
2189584 TTTTTTGAAA
*
2189594 TTTTGGTTTTTTTTTGCTTT
1 TTTTTGTTTTTTTTTGCTTT
2189614 TTTTTGTTTTTTTTTTTGCATTT
1 TTTTTG--TTTTTTTTTGC-TTT
2189637 TTTTTGTTTTTTGTTTG
1 TTTTTGTTTTTT-TTTG
2189654 AAAAAATAGC
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
20 5 0.14
21 6 0.17
22 15 0.43
23 9 0.26
ACGTcount: A:0.02, C:0.03, G:0.13, T:0.82
Consensus pattern (20 bp):
TTTTTGTTTTTTTTTGCTTT
Found at i:2196982 original size:19 final size:20
Alignment explanation
Indices: 2196939--2196990 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
2196929 GAAACCCCTT
2196939 TGAAAATACATGGTTTTTAAA
1 TGAAAATACAT-GTTTTTAAA
2196960 TGAAAATACAT-TATTTT-AA
1 TGAAAATACATGT-TTTTAAA
*
2196979 TGAAGATACATG
1 TGAAAATACATG
2196991 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 13 0.46
20 4 0.14
21 11 0.39
ACGTcount: A:0.44, C:0.06, G:0.13, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGTTTTTAAA
Found at i:2200075 original size:10 final size:9
Alignment explanation
Indices: 2200056--2200110 Score: 51
Period size: 10 Copynumber: 6.1 Consensus size: 9
2200046 CTTTTTGAAA
2200056 TTTTCTTTT
1 TTTTCTTTT
*
2200065 TTTTC-CTT
1 TTTTCTTTT
2200073 TTTTC-TTT
1 TTTTCTTTT
*
2200081 TTCTCTTCTT
1 TTTTCTT-TT
*
2200091 TTGTCTTTT
1 TTTTCTTTT
2200100 TCTTTCTTTT
1 T-TTTCTTTT
2200110 T
1 T
2200111 GTACTCCAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
8 13 0.34
9 9 0.24
10 16 0.42
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (9 bp):
TTTTCTTTT
Found at i:2200076 original size:17 final size:17
Alignment explanation
Indices: 2200056--2200110 Score: 76
Period size: 17 Copynumber: 3.2 Consensus size: 17
2200046 CTTTTTGAAA
2200056 TTTTCTTTTT-TTTCCTT
1 TTTTCTTTTTCTTT-CTT
2200073 TTTTCTTTTTCTCTTCTT
1 TTTTCTTTTTCT-TTCTT
*
2200091 TTGTCTTTTTCTTTCTT
1 TTTTCTTTTTCTTTCTT
2200108 TTT
1 TTT
2200111 GTACTCCAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 17 0.50
18 15 0.44
19 2 0.06
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (17 bp):
TTTTCTTTTTCTTTCTT
Found at i:2200111 original size:18 final size:18
Alignment explanation
Indices: 2200059--2200112 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
2200049 TTTGAAATTT
2200059 TCTTTTT-TTTCCTTTTT-
1 TCTTTTTCTTT-CTTTTTG
2200076 TCTTTTTCTCTTC-TTTTG
1 TCTTTTTCT-TTCTTTTTG
2200094 TCTTTTTCTTTCTTTTTG
1 TCTTTTTCTTTCTTTTTG
2200112 T
1 T
2200113 ACTCCAATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
17 14 0.42
18 17 0.52
19 2 0.06
ACGTcount: A:0.00, C:0.19, G:0.04, T:0.78
Consensus pattern (18 bp):
TCTTTTTCTTTCTTTTTG
Found at i:2200861 original size:19 final size:21
Alignment explanation
Indices: 2200818--2200869 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
2200808 GAAACCCCTT
2200818 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
2200839 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
2200858 TGAAGATACATG
1 TGAAAATACATG
2200870 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:2201199 original size:16 final size:16
Alignment explanation
Indices: 2201178--2201210 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2201168 TAGTTAGCTC
2201178 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
*
2201194 ATTTGCGTTCTAACAT
1 ATTTGCATTCTAACAT
2201210 A
1 A
2201211 GGTGGCAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.18, G:0.09, T:0.42
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:2203022 original size:33 final size:33
Alignment explanation
Indices: 2202945--2203048 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
2202935 ATACAATCTG
* * *
2202945 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATTACCA-TATCACGCCAATAACATCATCC---T
2202981 TCCATTACCATATCACGCCAATAACATCATCCT
1 TCCATTACCATATCACGCCAATAACATCATCCT
* * *
2203014 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATTACCATATCA-CGCCAATAACATCATCCT
2203047 TC
1 TC
2203049 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 25 0.42
34 7 0.12
35 17 0.28
36 11 0.18
ACGTcount: A:0.31, C:0.36, G:0.02, T:0.32
Consensus pattern (33 bp):
TCCATTACCATATCACGCCAATAACATCATCCT
Found at i:2207489 original size:33 final size:33
Alignment explanation
Indices: 2207410--2207513 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
2207400 ATACAATCTG
* *
2207410 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
2207446 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
2207479 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
2207512 TC
1 TC
2207514 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:2211956 original size:33 final size:33
Alignment explanation
Indices: 2211912--2211980 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
2211902 CATCACCATA
*
2211912 TTCCATCACCATATCA-CGCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
2211945 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
2211978 TTC
1 TTC
2211981 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.30, C:0.36, G:0.01, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:2215099 original size:16 final size:16
Alignment explanation
Indices: 2215075--2215107 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2215065 TAGTTAGCTC
2215075 ATTTACATTCTAACAT
1 ATTTACATTCTAACAT
*
2215091 ATTTGCATTCTAACAT
1 ATTTACATTCTAACAT
2215107 A
1 A
2215108 GGTGGCAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.18, G:0.03, T:0.42
Consensus pattern (16 bp):
ATTTACATTCTAACAT
Found at i:2216878 original size:19 final size:20
Alignment explanation
Indices: 2216854--2216893 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
2216844 TATCCTTTCT
2216854 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
2216873 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
2216893 T
1 T
2216894 ATTATTATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:2217224 original size:14 final size:13
Alignment explanation
Indices: 2217205--2217270 Score: 55
Period size: 13 Copynumber: 4.8 Consensus size: 13
2217195 TTTCTTTTGA
2217205 CTTTTCTTCTTTTT
1 CTTTTCTT-TTTTT
2217219 CTTTTCTTTTTTT
1 CTTTTCTTTTTTT
*
2217232 CTGAATTT-TTTTCTT
1 CT---TTTCTTTTTTT
*
2217247 CTTTT-TGTCTTTT
1 CTTTTCT-TTTTTT
2217260 CTTTTCTTTTT
1 CTTTTCTTTTT
2217271 GTACTCCAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
12 4 0.09
13 19 0.44
14 9 0.21
15 8 0.19
16 3 0.07
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.77
Consensus pattern (13 bp):
CTTTTCTTTTTTT
Found at i:2217259 original size:18 final size:18
Alignment explanation
Indices: 2217205--2217272 Score: 66
Period size: 19 Copynumber: 3.7 Consensus size: 18
2217195 TTTCTTTTGA
*
2217205 CTTTTCTTCTTTTTCTTTT
1 CTTTTCTT-TTTGTCTTTT
* **
2217224 CTTTT-TTTCTGAATTTT
1 CTTTTCTTTTTGTCTTTT
*
2217241 TTTCTTCTTTTTGTCTTTT
1 CTT-TTCTTTTTGTCTTTT
2217260 CTTTTCTTTTTGT
1 CTTTTCTTTTTGT
2217273 ACTCCAATTT
Statistics
Matches: 38, Mismatches: 9, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
17 8 0.21
18 14 0.37
19 16 0.42
ACGTcount: A:0.03, C:0.16, G:0.04, T:0.76
Consensus pattern (18 bp):
CTTTTCTTTTTGTCTTTT
Found at i:2221973 original size:28 final size:28
Alignment explanation
Indices: 2221941--2222014 Score: 88
Period size: 24 Copynumber: 2.8 Consensus size: 28
2221931 TAATTGTTGA
2221941 TGAGTGCTTCAACTTCTTTTCTTTCTTT
1 TGAGTGCTTCAACTTCTTTTCTTTCTTT
2221969 TGAGTGC-T-AGA--T-TTTTCTTTCTTT
1 TGAGTGCTTCA-ACTTCTTTTCTTTCTTT
2221993 TGAGTGCTTC-ACTTTCTTTTCT
1 TGAGTGCTTCAAC-TTCTTTTCT
2222015 GATTTTTTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
24 20 0.51
25 2 0.05
26 1 0.03
27 3 0.08
28 13 0.33
ACGTcount: A:0.11, C:0.19, G:0.14, T:0.57
Consensus pattern (28 bp):
TGAGTGCTTCAACTTCTTTTCTTTCTTT
Found at i:2225958 original size:25 final size:25
Alignment explanation
Indices: 2225905--2225964 Score: 74
Period size: 24 Copynumber: 2.5 Consensus size: 25
2225895 CTTTTCTTTG
2225905 CTTTTTC-TTCTTTTTGAGTGCTGTA
1 CTTTTTCTTTC-TTTTGAGTGCTGTA
2225930 -TTTTTCTTTCTTTTGAGTGCT-TCA
1 CTTTTTCTTTCTTTTGAGTGCTGT-A
2225954 CTTTTT-TTTCT
1 CTTTTTCTTTCT
2225965 GATTTTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
23 1 0.03
24 23 0.72
25 8 0.25
ACGTcount: A:0.07, C:0.17, G:0.12, T:0.65
Consensus pattern (25 bp):
CTTTTTCTTTCTTTTGAGTGCTGTA
Found at i:2230504 original size:5 final size:5
Alignment explanation
Indices: 2230487--2230516 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
2230477 CCTCAAAAAG
*
2230487 AAGAA AAGCA AAGAA AAGAA AAGAA AAGAA
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA
2230517 GTTGAAGCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.77, C:0.03, G:0.20, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:2231158 original size:19 final size:19
Alignment explanation
Indices: 2231130--2231167 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2231120 GAAAACACAT
* *
2231130 ATTTTTATGAAGATTCATG
1 ATTTTAATGAAAATTCATG
2231149 ATTTTAATGAAAATTCATG
1 ATTTTAATGAAAATTCATG
2231168 CCTTAGGCCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.45
Consensus pattern (19 bp):
ATTTTAATGAAAATTCATG
Found at i:2240596 original size:44 final size:44
Alignment explanation
Indices: 2240525--2240841 Score: 330
Period size: 44 Copynumber: 7.2 Consensus size: 44
2240515 AAACCGAGTT
* * * *
2240525 CATAACTGAAATGCATACTAGTGCATTAAGACATAAAAGGATGC
1 CATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGC
* * * *
2240569 CATAACTGAAAGGCATCATGGTTCATTAAGGCATGTAAGGATGC
1 CATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGC
* * * *
2240613 CACAACTGAAATGCATAACGGTGCATTAAGGCATGAAATGATGA
1 CATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGC
* ** * * * *
2240657 CACATTTGAAATGCATAACGGCGTATTAAGGCATGAAATGATGC
1 CATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGC
* * *
2240701 CATAACTGAAATACATAATGGTGCATTAAGACATGAAAGG-TTC
1 CATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGC
* * *
2240744 TATAACTGATATGCATAATGGTGCATTAAGGCATGAAATGATGC
1 CATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGC
* * ** * * *
2240788 GATAAATGAAATGCATAACAGTACAATAAGGCATGAAATGATGC
1 CATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGC
*
2240832 CATAAATGAA
1 CATAACTGAA
2240842 GATAATAAAT
Statistics
Matches: 227, Mismatches: 45, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
43 37 0.16
44 190 0.84
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.24
Consensus pattern (44 bp):
CATAACTGAAATGCATAATGGTGCATTAAGGCATGAAAGGATGC
Found at i:2240800 original size:131 final size:132
Alignment explanation
Indices: 2240531--2240849 Score: 358
Period size: 131 Copynumber: 2.4 Consensus size: 132
2240521 AGTTCATAAC
** * * * ** * *
2240531 TGAAATGCAT-ACTAGTGCATTAAGACATAAAAGGATGCCATAACTGAAAGGCATCATGGTTCAT
1 TGAAATGCATAAC-AGCACATTAAGGCATGAAATGATGCCATAACTGAAATACATAATGGTGCAT
* *
2240595 TAAGGCATGTAAGGATGCCACAACTGAAATGCATAACGGTGCATTAAGGCATGAAATGATGACAC
65 TAAGACATGAAAGGATGCCACAACTGAAATGCATAACGGTGCATTAAGGCATGAAATGATGACAC
**
2240660 ATT
130 AAA
* **
2240663 TGAAATGCATAACGGCGTATTAAGGCATGAAATGATGCCATAACTGAAATACATAATGGTGCATT
1 TGAAATGCATAACAGCACATTAAGGCATGAAATGATGCCATAACTGAAATACATAATGGTGCATT
* * * * * *
2240728 AAGACATGAAAGG-TTCTATAACTGATATGCATAATGGTGCATTAAGGCATGAAATGATG-CGAT
66 AAGACATGAAAGGATGCCACAACTGAAATGCATAACGGTGCATTAAGGCATGAAATGATGAC-AC
2240791 AAA
130 AAA
* * *
2240794 TGAAATGCATAACAGTACAATAAGGCATGAAATGATGCCATAAATGAAGATA-ATAA
1 TGAAATGCATAACAGCACATTAAGGCATGAAATGATGCCATAACTGAA-ATACATAA
2240850 ATAATTACTA
Statistics
Matches: 158, Mismatches: 26, Indels: 7
0.83 0.14 0.04
Matches are distributed among these distances:
130 1 0.01
131 89 0.56
132 66 0.42
133 2 0.01
ACGTcount: A:0.41, C:0.13, G:0.21, T:0.24
Consensus pattern (132 bp):
TGAAATGCATAACAGCACATTAAGGCATGAAATGATGCCATAACTGAAATACATAATGGTGCATT
AAGACATGAAAGGATGCCACAACTGAAATGCATAACGGTGCATTAAGGCATGAAATGATGACACA
AA
Found at i:2250024 original size:81 final size:81
Alignment explanation
Indices: 2249889--2250055 Score: 282
Period size: 81 Copynumber: 2.1 Consensus size: 81
2249879 GTTCTTAAAA
*
2249889 TAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGCCAATATTGCAAGTTAGATGAAAG
2249954 GCTAAATGCC-TTCGAG
66 GCTAAATGCCATT-GAG
* * *
2249970 TAAAAGATTAATTGCCTAGCTGTGTATTTGACATAACGGTGCCAATATTGCAAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGCCAATATTGCAAGTTAGATGAAAG
2250035 GCTAAATGCCATTGAG
66 GCTAAATGCCATTGAG
2250051 TAAAA
1 TAAAA
2250056 TACTTTGAGT
Statistics
Matches: 81, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
81 79 0.98
82 2 0.02
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (81 bp):
TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGCCAATATTGCAAGTTAGATGAAAG
GCTAAATGCCATTGAG
Found at i:2250130 original size:95 final size:95
Alignment explanation
Indices: 2249967--2250150 Score: 289
Period size: 95 Copynumber: 1.9 Consensus size: 95
2249957 AAATGCCTTC
* * *
2249967 GAGTAAAAGATTAATTGCCTAGCTGTGTATTTGACATAACGGTGCCAATATTGCAAGTTAGATGA
1 GAGTAAAAGATTAATTACCTAGCTGTGCATTTGACATAACAGTGCCAATATTGCAAGTTAGATGA
*
2250032 AAGGCTAAATGCCATTGAGTAAAATACTTT
66 AAGGATAAATGCCATTGAGTAAAATACTTT
* *
2250062 GAGTAAAAGATTAATTACCTAGCTGTGCATTTGGCATATA-AGTGTCAATATTGCAAGTTAGATG
1 GAGTAAAAGATTAATTACCTAGCTGTGCATTTGACATA-ACAGTGCCAATATTGCAAGTTAGATG
*
2250126 AAAGGATAAATGCCTTTGAGTAAAA
65 AAAGGATAAATGCCATTGAGTAAAA
2250151 GATTAATTGT
Statistics
Matches: 81, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
95 80 0.99
96 1 0.01
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.30
Consensus pattern (95 bp):
GAGTAAAAGATTAATTACCTAGCTGTGCATTTGACATAACAGTGCCAATATTGCAAGTTAGATGA
AAGGATAAATGCCATTGAGTAAAATACTTT
Found at i:2250393 original size:81 final size:81
Alignment explanation
Indices: 2250058--2250448 Score: 560
Period size: 81 Copynumber: 4.9 Consensus size: 81
2250048 GAGTAAAATA
* * *
2250058 CTTTGAGTAAAAGATTAATTACCTAGCTGTGCATTTGGCATATAA-GTGTCAATATTGCAAGTTA
1 CTTTGAGTAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGA-AAGGTGCCAATATTGCAAGTTA
*
2250122 GATGAAAGGATAAATGC
65 GATGAAAGGCTAAATGC
* *
2250139 CTTTGAGTAAAAGATTAATTGTCTAGCT-TGCATTTGGCATAAAGGTGCCAATATTGC-A-TTAG
1 CTTTGAGTAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAG
2250201 ATGAAAGGCTAAATGC
66 ATGAAAGGCTAAATGC
* * *
2250217 CTTTGAGTAAAAGATTAGTTGCCTAGCTGTGCATTTGGTAG-AAGCG-ACCAATATTGCAAGTTA
1 CTTTGAGTAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAAG-GTGCCAATATTGCAAGTTA
2250280 GATGAAAGGCTAAATGC
65 GATGAAAGGCTAAATGC
* *
2250297 CTTTGAGTAAAAGATTAATTGCCTAGCTGTGTATTTGGCAGAAAGGGGCCAATATTGCAAGTTAG
1 CTTTGAGTAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAG
2250362 ATGAAAGGCTAAATGC
66 ATGAAAGGCTAAATGC
* * * * *
2250378 CTTTGAGTAAAAGATTAAGTGCCTAGTTGTGCATTATTGGTAGAAAGGTGCCATTAATGCAAGTT
1 CTTTGAGTAAAAGATTAATTGCCTAGCTGTGCA-T-TTGGCAGAAAGGTGCCAATATTGCAAGTT
2250443 AGATGA
64 AGATGA
2250449 TAACTGTGCT
Statistics
Matches: 281, Mismatches: 20, Indels: 16
0.89 0.06 0.05
Matches are distributed among these distances:
78 58 0.21
79 15 0.05
80 84 0.30
81 92 0.33
82 1 0.00
83 31 0.11
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.31
Consensus pattern (81 bp):
CTTTGAGTAAAAGATTAATTGCCTAGCTGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAG
ATGAAAGGCTAAATGC
Found at i:2276011 original size:15 final size:15
Alignment explanation
Indices: 2275972--2276013 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
2275962 ATGCTTATTT
*
2275972 TATAGTTATTTTATC
1 TATAGTTATTATATC
*
2275987 TACA-TATATTATATC
1 TATAGT-TATTATATC
2276002 TATAGTTATTAT
1 TATAGTTATTAT
2276014 GATGATAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
14 1 0.05
15 20 0.91
16 1 0.05
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (15 bp):
TATAGTTATTATATC
Found at i:2277339 original size:19 final size:20
Alignment explanation
Indices: 2277315--2277354 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
2277305 TATCCTTTCT
2277315 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
2277334 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
2277354 T
1 T
2277355 ATTATTATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:2279651 original size:11 final size:12
Alignment explanation
Indices: 2279622--2279661 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
2279612 TTTGGTACTG
2279622 GAAACAAGATAA
1 GAAACAAGATAA
*
2279634 GAAACAAGATTA
1 GAAACAAGATAA
2279646 -AAACAAGATAAA
1 GAAACAAGAT-AA
2279658 GAAA
1 GAAA
2279662 TTGAAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 9 0.38
12 12 0.50
13 3 0.12
ACGTcount: A:0.68, C:0.07, G:0.15, T:0.10
Consensus pattern (12 bp):
GAAACAAGATAA
Found at i:2281043 original size:17 final size:18
Alignment explanation
Indices: 2281021--2281054 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2281011 AGATACAACA
*
2281021 TCATCACCATC-TCCATT
1 TCATCAACATCATCCATT
2281038 TCATCAACATCATCCAT
1 TCATCAACATCATCCAT
2281055 CAGGACCATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.29, C:0.38, G:0.00, T:0.32
Consensus pattern (18 bp):
TCATCAACATCATCCATT
Found at i:2281139 original size:23 final size:26
Alignment explanation
Indices: 2281092--2281143 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
2281082 TATCCTTTTT
*
2281092 TTATTTCATTTCATTTCTTATCTTTA
1 TTATTTCATTTCATTTCTTACCTTTA
2281118 TTATTTCATTT-A-TTCTT-CCTTTA
1 TTATTTCATTTCATTTCTTACCTTTA
2281141 TTA
1 TTA
2281144 ATCATCTTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 8 0.32
24 5 0.20
25 1 0.04
26 11 0.44
ACGTcount: A:0.19, C:0.15, G:0.00, T:0.65
Consensus pattern (26 bp):
TTATTTCATTTCATTTCTTACCTTTA
Found at i:2288379 original size:21 final size:21
Alignment explanation
Indices: 2288331--2288379 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
2288321 AAGGAGTTGA
*
2288331 AAGGTAGCTGACACTAGTTAG
1 AAGGTAGCTGACACTAATTAG
* *
2288352 -AGAGTAGCTGACATTAATTGG
1 AAG-GTAGCTGACACTAATTAG
2288373 AAGGTAG
1 AAGGTAG
2288380 ATGAGGACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 2 0.09
21 19 0.83
22 2 0.09
ACGTcount: A:0.35, C:0.10, G:0.31, T:0.24
Consensus pattern (21 bp):
AAGGTAGCTGACACTAATTAG
Found at i:2290241 original size:12 final size:12
Alignment explanation
Indices: 2290209--2290248 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
2290199 CAATTACTTT
*
2290209 ATCTTATCTTT-
1 ATCTTATTTTTA
*
2290220 ATCTTTTTTTTA
1 ATCTTATTTTTA
2290232 ATCTTATTTTTA
1 ATCTTATTTTTA
2290244 ATCTT
1 ATCTT
2290249 GTTTCCAGCA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
11 9 0.36
12 16 0.64
ACGTcount: A:0.20, C:0.12, G:0.00, T:0.68
Consensus pattern (12 bp):
ATCTTATTTTTA
Done.